VCF file format for VCFTOOLs

Question

[syxsu]

I used PLINK to generate a vcf and want to use vcftools to analyze it. Here is the first several line of the vcf files:

##fileformat=VCFv4.2
##fileDate=20220520
##source=PLINKv1.90
##contig=<ID=0,length=2147483645
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome"
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  14LM0008_14LM0008   14...**

When I run vcftools, I get the error code:

Error: Unknown option: ##fileDate=20220520

After I delete the first several lines, the new error code occurs:

Error: Unknown option: ##POS

Here is my code:

vcftools --vcf $file --keep $list --max-missing 0.8 --hwe 0.1 --relatedness2 --out ${name}maxmissing.vcf

My vcftools version is 0.1.15

I wonder why this will happen.

[iraun]

Have you tried FixVcfHeader yo try to sanity check the VCFs?

[Pierre Lindenbaum]

what is the output of

echo vcftools --vcf "$file" --keep "$list" --max-missing 0.8 --hwe 0.1 --relatedness2 --out "${name}maxmissing.vcf"
file $file
file $list